Advanced search
1 file | 1.38 MB

Small-scale gene duplications played a major role in the recent evolution of wheat chromosome 3B

Author
Organization
Project
Bioinformatics: from nucleotids to networks (N2N)
Abstract
Background: Bread wheat is not only an important crop, but its large (17 Gb), highly repetitive, and hexaploid genome makes it a good model to study the organization and evolution of complex genomes. Recently, we produced a high quality reference sequence of wheat chromosome 3B (774 Mb), which provides an excellent opportunity to study the evolutionary dynamics of a large and polyploid genome, specifically the impact of single gene duplications. Results: We find that 27 % of the 3B predicted genes are non-syntenic with the orthologous chromosomes of Brachypodium distachyon, Oryza sativa, and Sorghum bicolor, whereas, by applying the same criteria, non-syntenic genes represent on average only 10 % of the predicted genes in these three model grasses. These non-syntenic genes on 3B have high sequence similarity to at least one other gene in the wheat genome, indicating that hexaploid wheat has undergone massive small-scale interchromosomal gene duplications compared to other grasses. Insertions of non-syntenic genes occurred at a similar rate along the chromosome, but these genes tend to be retained at a higher frequency in the distal, recombinogenic regions. The ratio of non-synonymous to synonymous substitution rates showed a more relaxed selection pressure for non-syntenic genes compared to syntenic genes, and gene ontology analysis indicated that non-syntenic genes may be enriched in functions involved in disease resistance. Conclusion: Our results highlight the major impact of single gene duplications on the wheat gene complement and confirm the accelerated evolution of the Triticeae lineage among grasses.
Keywords
SEQUENCE, BARLEY, GENOME EVOLUTION, PLANT GENOMES, RECOMBINATION, ORGANIZATION, ALIGNMENT, RICE, GRASSES, TRANSPOSABLE ELEMENTS

Downloads

  • Glover et al. 2015 Genome Biology 16 188.pdf
    • full text
    • |
    • open access
    • |
    • PDF
    • |
    • 1.38 MB

Citation

Please use this url to cite or link to this publication:

Chicago
Glover, Natasha M, Josquin Daron, Lise Pingault, Klaas Vandepoele, Etienne Paux, Catherine Feuillet, and Frédéric Choulet. 2015. “Small-scale Gene Duplications Played a Major Role in the Recent Evolution of Wheat Chromosome 3B.” Genome Biology 16.
APA
Glover, N. M., Daron, J., Pingault, L., Vandepoele, K., Paux, E., Feuillet, C., & Choulet, F. (2015). Small-scale gene duplications played a major role in the recent evolution of wheat chromosome 3B. GENOME BIOLOGY, 16.
Vancouver
1.
Glover NM, Daron J, Pingault L, Vandepoele K, Paux E, Feuillet C, et al. Small-scale gene duplications played a major role in the recent evolution of wheat chromosome 3B. GENOME BIOLOGY. 2015;16.
MLA
Glover, Natasha M, Josquin Daron, Lise Pingault, et al. “Small-scale Gene Duplications Played a Major Role in the Recent Evolution of Wheat Chromosome 3B.” GENOME BIOLOGY 16 (2015): n. pag. Print.
@article{6951308,
  abstract     = {Background: Bread wheat is not only an important crop, but its large (17 Gb), highly repetitive, and hexaploid genome makes it a good model to study the organization and evolution of complex genomes. Recently, we produced a high quality reference sequence of wheat chromosome 3B (774 Mb), which provides an excellent opportunity to study the evolutionary dynamics of a large and polyploid genome, specifically the impact of single gene duplications. 
Results: We find that 27 \% of the 3B predicted genes are non-syntenic with the orthologous chromosomes of Brachypodium distachyon, Oryza sativa, and Sorghum bicolor, whereas, by applying the same criteria, non-syntenic genes represent on average only 10 \% of the predicted genes in these three model grasses. These non-syntenic genes on 3B have high sequence similarity to at least one other gene in the wheat genome, indicating that hexaploid wheat has undergone massive small-scale interchromosomal gene duplications compared to other grasses. Insertions of non-syntenic genes occurred at a similar rate along the chromosome, but these genes tend to be retained at a higher frequency in the distal, recombinogenic regions. The ratio of non-synonymous to synonymous substitution rates showed a more relaxed selection pressure for non-syntenic genes compared to syntenic genes, and gene ontology analysis indicated that non-syntenic genes may be enriched in functions involved in disease resistance. 
Conclusion: Our results highlight the major impact of single gene duplications on the wheat gene complement and confirm the accelerated evolution of the Triticeae lineage among grasses.},
  articleno    = {188},
  author       = {Glover, Natasha M and Daron, Josquin and Pingault, Lise and Vandepoele, Klaas and Paux, Etienne and Feuillet, Catherine and Choulet, Fr{\'e}d{\'e}ric},
  issn         = {1465-6906},
  journal      = {GENOME BIOLOGY},
  keyword      = {SEQUENCE,BARLEY,GENOME EVOLUTION,PLANT GENOMES,RECOMBINATION,ORGANIZATION,ALIGNMENT,RICE,GRASSES,TRANSPOSABLE ELEMENTS},
  language     = {eng},
  pages        = {13},
  title        = {Small-scale gene duplications played a major role in the recent evolution of wheat chromosome 3B},
  url          = {http://dx.doi.org/10.1186/s13059-015-0754-6},
  volume       = {16},
  year         = {2015},
}

Altmetric
View in Altmetric
Web of Science
Times cited: